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Merge dev changes #5

Merged
merged 13 commits into from
Sep 30, 2024
Merged

Merge dev changes #5

merged 13 commits into from
Sep 30, 2024

Commits on Jul 24, 2024

  1. Updates to vcf_mod.py 

    - Remove the older PID and PGT fields
- Output the AD annotations at more sites
- Make DP more consistent with the AD
    @DonFreed
    DonFreed committed Jul 24, 2024
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  2. Update README.md

    @DonFreed
    DonFreed committed Jul 24, 2024
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  3. Add mosdepth for alignment QC

    @DonFreed
    DonFreed committed Jul 24, 2024
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  4. Improve logging

    @DonFreed
    DonFreed committed Jul 24, 2024
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Commits on Aug 14, 2024

  1. Handle non-unicode output in version strings

    @DonFreed
    DonFreed committed Aug 14, 2024
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Commits on Sep 9, 2024

  1. Add support for haploid gVCFs

    @DonFreed
    DonFreed committed Sep 9, 2024
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  2. Create a single output VCF for snv and indels

    @DonFreed
    DonFreed committed Sep 9, 2024
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  3. Add a dockerfile

    @DonFreed
    DonFreed committed Sep 9, 2024
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  4. Update DNAscope default arguments

    @DonFreed
    DonFreed committed Sep 9, 2024
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Commits on Sep 17, 2024

  1. Add -Y to minimap2 by default 

    Expose `--minimap2_args` on the command line.
    @DonFreed
    DonFreed committed Sep 17, 2024
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Commits on Sep 30, 2024

  1. Install multiqc for the GH tests

    @DonFreed
    DonFreed committed Sep 30, 2024
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  2. Generalize the gvcf_combine script by ploidy

    @DonFreed
    DonFreed committed Sep 30, 2024
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  3. Update github actions

    @DonFreed
    DonFreed committed Sep 30, 2024
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